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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROAEROLYSIN MUTANT Y221G
 
Authors :  L. Pernot, M. Schiltz, S. Thurnheer, S. E. Burr, G. Van Der Goot
Date :  21 Jan 08  (Deposition) - 12 Feb 08  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Toxin, Cytolytic Toxin, Pore-Forming Toxin, Membrane, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Degiacomi, I. Iacovache, L. Pernot, M. Chami, M. Kudryashev, H. Stahlberg, F. G. Van Der Goot, M. Dal Peraro
Molecular Assembly Of The Aerolysin Pore Reveals A Swirling Membrane-Insertion Mechanism.
Nat. Chem. Biol. V. 9 623 2013
PubMed-ID: 23912165  |  Reference-DOI: 10.1038/NCHEMBIO.1312
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AEROLYSIN
    Chains: A, B
    Engineered: YES
    Expression System: AEROMONAS SALMONICIDA
    Expression System Plasmid: PMMB66EH
    Expression System Strain: CD3
    Expression System Taxid: 645
    Expression System Vector Type: PLASMID
    Gene: AERA
    Mutation: YES
    Organism Scientific: AEROMONAS HYDROPHILA
    Organism Taxid: 644

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3C0M)

(-) Sites  (0, 0)

(no "Site" information available for 3C0M)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:75
2A:159 -A:164
3B:19 -B:75
4B:159 -B:164

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C0M)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AEROLYSINPS00274 Aerolysin type toxins signature.AERA_AERHY246-255
 		  2A:223-232
B:223-232

(-) Exons   (0, 0)

(no "Exon" information available for 3C0M)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:449
 aligned with AERA_AERHY | P09167 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:467
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
           AERA_AERHY    25 EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAHYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVTTKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDKRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPLAADSKVRRARSVDGAGQGLRLEIPLDAQELSGLGFNNVSLSVTPAA 491
               SCOP domains d3c0ma1 A:2-84 Proaerolysin, N-terminal domain                                     d3c0ma2 A:85-468 (Pro)aerolysin, pore-forming lobe                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3c0mA01 A:2-90 Pertussis Toxin, subunit B, domain 1                                      3c0mA02 A:91-176,A:311-397 Proaerolysin, chain A, domain 2                            3c0mA03 A:177-310,A:398-468 Proaerolysin, chain A, domain 3                                                                           3c0mA02 A:91-176,A:311-397 Proaerolysin, chain A, domain 2                             3c0mA03 A:177-310,A:398-4                  68 Proaerolysin, chain A, do CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheeee.........eee.hhhhhhhhhhhhhh......eee....eeee.hhhh..eee....eeeeee.............eee...hhhhhhhhhhh....hhhhhhhhhhhhh...............eeeeee..eeeeee...............eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee........eeeeeeeeeeeeeee....hhhh.ee....ee...........ee..........eeeeeeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee................eeeeeeee....hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeeeeeee...ee.------------------.eee...hhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AEROLYSIN -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0m A   2 EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAHYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRGDTATNWSKTNTYGLSEKVTTKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDKRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPL------------------LRLEIPLDAQELSGLGFNNVSLSVTPAA 468
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421|        -       441       451       461       
                                                                                                                                                                                                                                                                                                                                                                                                                                                              422                441                           


Chain B from PDB  Type:PROTEIN  Length:449
 aligned with AERA_AERHY | P09167 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:467
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
           AERA_AERHY    25 EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAHYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVTTKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDKRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPLAADSKVRRARSVDGAGQGLRLEIPLDAQELSGLGFNNVSLSVTPAA 491
               SCOP domains d3c0mb1 B:2-84 Proaerolysin, N-terminal domain                                     d3c0mb2 B:85-468 (Pro)aerolysin, pore-forming lobe                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3c0mB01 B:2-90 Pertussis Toxin, subunit B, domain 1                                      3c0mB02 B:91-176,B:311-397 Proaerolysin, chain A, domain 2                            3c0mB03 B:177-310,B:398-468 Proaerolysin, chain A, domain 3                                                                           3c0mB02 B:91-176,B:311-397 Proaerolysin, chain A, domain 2                             3c0mB03 B:177-310,B:398-4                  68 Proaerolysin, chain A, do CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheeee.........eee.hhhhhhhhhhhhhh......eee....eeee.hhhh..eee....eeeeee.............eee...hhhhhhhhhhh....hhhhhhhhhhhhh...............eeeeee..eeeeee...............eeeeeeeeeee.hhhhee.....eeeeeeeeeeeeeee........eeeeeeeeeeeeeeeee..hhhhhh.....ee...........ee....hhhhh.eeeeeeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee................eeeeeeee........hhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeee...ee...ee.------------------.ee....hhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AEROLYSIN -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c0m B   2 EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAHYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRGDTATNWSKTNTYGLSEKVTTKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDKRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPL------------------LRLEIPLDAQELSGLGFNNVSLSVTPAA 468
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421|        -       441       451       461       
                                                                                                                                                                                                                                                                                                                                                                                                                                                              422                441
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C0M)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AERA_AERHY | P09167)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  3c0m
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AERA_AERHY | P09167: 1pre 1z52 3c0n 3c0o 3g4n 3g4o 5jzh 5jzt 5jzw

(-) Related Entries Specified in the PDB File

1pre WILD-TYPE PROAEROLYSIN
3c0n CRYSTAL STRUCTURE OF THE PROAEROLYSIN MUTANT Y221G AT 2.2 A
3c0o CRYSTAL STRUCTURE OF THE PROAEROLYSIN MUTANT Y221G COMPLEXED WITH MANNOSE-6-PHOSPHATE